1.1 Read quality

1.2 Read counts

1.3 Read decontamination

Reads removed because they matched one of the pre-specified host/contaminant genomes are grouped into the ‘Host/Contaminant’ category. Reads removed due to low complexity or quality are grouped into the ‘Low Quality’ category.

2.1 Phylum-level heatmaps

Showing taxa at the phyla level or higher that appear in at least 4 samples.

2.2 Genus-level heatmap

Showing taxa at the genus level or higher that appear in at least 4 samples.

2.3 Species-level heatmap

Showing all species level annotations for all samples. Warning: this plot can be quite large.